A change management method and system for tool-based document generation which incorporates tool input changes, tool changes, and user changes during iterative document creation. After a tool-based document is generated and saved by a tool, and then edited by a user, during a next iteration of creating the edited document, the tool first generates a new base document. The base document is then saved, and a three-way merge is performed on the former iteration's base document, this iteration's new base document, and the former iteration's edited document. The former iteration's base document serves as the base of the merge process. The merge outputs a merged document, and when further edits are needed, the merged document is edited, and saved as the edited document. If no edits are necessary, the merged document is saved directly as the edited document. In each iteration, the new base document and the edited document are saved for a possible next iteration.